rbbt-GE 1.0.0 → 1.1.0

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@@ -0,0 +1,15 @@
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data/LICENSE CHANGED
@@ -1,4 +1,4 @@
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- Copyright (c) 2010-2011 Miguel Vázquez García
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+ Copyright (c) 2010-2013 Miguel Vázquez García
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  Permission is hereby granted, free of charge, to any person obtaining
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  a copy of this software and associated documentation files (the
data/lib/rbbt/GE.rb CHANGED
@@ -5,8 +5,8 @@ module GE
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  MA = File.join(LIB_DIR, 'MA.R')
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  def self.run_R(command)
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- cmd = "source('#{MA}');" << command
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- R.run(cmd)
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+ cmd = "\nsource('#{MA}');\n" << command
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+ R.run(cmd, :monitor => true)
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  end
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  def self.r_format(list, options = {})
@@ -35,5 +35,11 @@ module GE
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  FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
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  GE.run_R("rbbt.GE.process(#{ r_format datafile }, main = #{r_format(main, :strings => true)}, contrast = #{r_format(contrast, :strings => true)}, log2=#{ r_format log2 }, outfile = #{r_format outfile}, key.field = #{r_format key_field}, two.channel = #{r_format two_channel})")
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  end
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+
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+ def self.barcode(datafile, outfile, factor = 2)
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+ FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
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+ GE.run_R("rbbt.GE.barcode(#{ r_format datafile }, #{ r_format outfile }, #{ r_format factor })")
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+ end
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+
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  end
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data/lib/rbbt/GE/GEO.rb CHANGED
@@ -142,6 +142,7 @@ module GEO
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  def self.parse_header(stream, info)
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  header = ""
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  while line = stream.readline
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+ line = Misc.fixutf8 line
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  header << line
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  break if line =~ /^#{info[:DELIMITER]}/i
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  raise "Delimiter not found" if stream.eof?
data/share/lib/R/MA.R CHANGED
@@ -1,5 +1,35 @@
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  library(limma)
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+ #########################################################################
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+ # BARCODE
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+
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+ rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2){
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+ data = rbbt.tsv(matrix_file)
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+ data.mean = rowMeans(data, na.rm=T)
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+ data.sd = apply(data, 1, sd, na.rm=T)
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+ data.threshold = as.matrix(data.mean) + sd.factor * as.matrix(data.sd)
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+ names(data.threshold) = names(data.mean)
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+ rm(data.mean)
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+ rm(data.sd)
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+
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+ file.barcode = file(output_file, 'w')
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+
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+ cat("#Ensembl Gene ID", file = file.barcode)
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+ cat("\t", file = file.barcode)
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+ cat(colnames(data), file = file.barcode, sep="\t")
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+ cat("\n", file = file.barcode)
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+
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+ for (gene in rownames(data)){
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+ barcode = (data[gene,] - data.threshold[gene]) > 0
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+
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+ cat(gene, file = file.barcode)
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+ cat("\t", file = file.barcode)
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+ cat(barcode, file = file.barcode, sep = "\t")
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+ cat("\n", file = file.barcode)
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+ }
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+ close(file.barcode)
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+ }
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+
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  #########################################################################
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  # Model processing
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@@ -529,6 +559,4 @@ MA.load <- function(prefix, orders = TRUE, logratios = TRUE, t = TRUE, p.values
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  return(data);
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-
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-
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  }
metadata CHANGED
@@ -1,20 +1,18 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-GE
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  version: !ruby/object:Gem::Version
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- version: 1.0.0
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- prerelease:
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+ version: 1.1.0
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-12-21 00:00:00.000000000 Z
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+ date: 2013-10-21 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rbbt-util
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  requirement: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
@@ -39,32 +36,31 @@ files:
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  - lib/rbbt/GE/GEO.rb
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  - share/install/GEO/Rakefile
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  - share/lib/R/MA.R
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- - test/test_helper.rb
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  - test/rbbt/GE/test_GEO.rb
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+ - test/test_helper.rb
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  homepage: http://github.com/mikisvaz/rbbt-GE
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  licenses: []
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+ metadata: {}
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  post_install_message:
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  rdoc_options: []
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  required_rubygems_version: !ruby/object:Gem::Requirement
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- none: false
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  requirements:
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  - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.8.24
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+ rubygems_version: 2.0.3
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  signing_key:
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- specification_version: 3
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+ specification_version: 4
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  summary: Gene Expression in RBBT
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  test_files:
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- - test/test_helper.rb
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  - test/rbbt/GE/test_GEO.rb
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+ - test/test_helper.rb